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The difficulty in proving the exact nature of prethermal reactions is that they occur too fast for standard solid-state chemical methods. One attractive idea was expressed by Harbottle 29), namely that, if a strong isotope effect is shown, very little subsequent chemical influence can have been felt and the observed species must have been formed by prethermal processes. The supposition here is that isotopic differences come only from differences in the nuclear deexcitation pattern (total energy, y-ray cascades, angular... 

We used modifications of the standard solid-state CP-MAS (cross-polarisation, magic-angle spinning) experiment to allow the proton relaxation characteristics to be measured for each peak in the C spectrum. It is known that highly mobile, hydrated polymers can not be seen using either usual CP-MAS C spectrum or solution NMR (6). We found, however, that by a combination of a long-contact experiment and a delayed-contact experiment we could reconstruct a C spectrum of the cell-wall components that are normally too mobile to be visible. With these techniques we were able to determine the mobility of pectins and their approximate spatial location in comparison to cellulose. 

Analytical Methods. Liquid scintillation counting (LSC) was done using Packard Models 3375 and 3380 Liquid Scintillation Spectrometers equipped with automatic external standards. Solid samples were combusted in a Packard model 306 Sample Oxidizer prior to LSC analysis. 

Using the OPENCORE NMR spectrometer, standard solid-state NMR experiments have been demonstrated in Ref. 2. They include 1H-13C CPMAS with TPPM decoupling, 13C-15N dipolar recoupling under MAS, 1H FSLG, 13C-13C 2D exchange, and so on. Here we show two more examples, where the spectrometer was used to implement standard pulse sequences, but in somewhat demanding circumstances in terms of sensitivity. 

The spectrometer supports phase cycling, asynchronous sequence implementation, and parameter-array experiments. Thus, most standard solid-state NMR experiments are feasible, including CPMAS, multiple-pulse H decoupling such as TPPM, 2D experiments, multiple-quantum NMR, and so on. In addition, the focus of development is on its extension of, or modification to, the hardware and/or the software, in the spirit of enabling the users to put their own new ideas into practice. In this paper, several examples of such have been described. They include the compact NMR and MRI systems, active compensation of RF pulse transients, implementation of a network analyzer, dynamic receiver-gain increment,31 and so on. 

The functionalization of commercially available standard solid supports is of particular interest for combinatorial purposes to enable a broad range of reactions to be studied. Since these transformations usually require long reaction times under conventional thermal conditions, it was obvious to combine microwave chemistry with the art of resin functionalization. 

In the chemical communication many peptide-protein (e.g., peptide hormone agonist) or protein-protein signaling interaction take place. Various photoreactive amino acids, e.g., azido-phenyalanines (Apa, TFApa) [40, 41], benzoyl-phenyalanines (Bpa,p-OH-Bpa) [41,42],trifluorometil-diazirine-phenylalanine (TMDPhe) [43], were developed (Fig. 3), which can be incorporated into any places in peptide sequences by standard solid-phase synthetic techniques. 

The studies with barbiturates revealed that the logarithm of the retention time is linearly related to the octanol/water partition coefficients [66,67]. It has been observed that the retention index of the drug is linearly related to the octanol/water partition coefficient (logP), and that results are very close to that of the 2-keto alkane standard (solid line in Fig. 15.9). 

By analogy to the solution-phase approaches, the introduction of lipid functionalities on peptides on the solid support can also follow two general approaches, either using prelipidated building blocks in the standard solid-phase peptide synthesis or via selective lipidation on resin. " " ... 

More recently, the Pam amino acid chimera has also been incorporated into a small j0j0a-motif peptide scaffold [28]. The family of BBA peptides was developed in our laboratory as structured platforms for the design of functional motifs. These motifs are attractive because they are small enough (23 residues) to be easily synthesized by standard solid phase synthesis methods. Additionally, the motifs appear to possess sufficient structural complexity to influence coenzyme properties while still being amenable to structural characterization by standard spectroscopic techniques [3, 29, 30]. The BBA peptides include a -hairpin domain with a type IT turn connected by a loop region to an a-heli-cal domain (Fig. 10). Packing of the sheet and helix against one another is accomplished by hydrophobic contacts created by a hydrophobic core of residues. 

Use of Proteases in Peptide Synthesis. Typically peptides are synthesized the standard solid or liquid phase methodologies (56, 57). However, both of these techniques require harsh chemical reactions which are detrimental to certain amino acids. Furthermore, in practical terms most peptide syntheses are limited to the range of 30 to 50 amino acid residues. Hence, peptide synthesis is still somewhat problematic in many cases. In certain situations, the alternative method of peptide synthesis using proteases is an attractive choice. With this form of synthesis, one can avoid the use of the noxious and hazardous chemicals used in solid or liquid phase peptide synthesis. Since the reactions are enzyme catalyzed, racemization of the peptide bond does not occur. This technique has been used with success in the synthesis and semisynthesis of several important peptides including human insulin (55,59). 

Our first foray into the realm of numerical convergence takes us away from the comfortable three-dimensional physical space where atom positions are defined and into what is known as reciprocal space. The concepts associated with reciprocal space are fundamental to much of solid-state physics that there are many physicists who can barely fathom the possibility that anyone might find them slightly mysterious. It is not our aim here to give a complete description of these concepts. Several standard solid-state physics texts that cover these topics in great detail are listed at the end of the chapter. Here, we aim to cover what we think are the most critical ideas related to how reciprocal space comes into practical DFT calculations, with particular emphasis on the relationship between these ideas and numerical convergence. 

As we have shown in Chapters 2 and 3, under the normal operating conditions of STM, the tunneling current can be calculated from the wavefunctions a few A from the outermost nuclei of the tip and the sample. The wavefunctions at the surfaces of solids, rather than the wavefunctions in the bulk, contribute to the tunneling current. In this chapter, we will discuss the general properties of the wavefunctions at surfaces. This is to fill the gap between standard solid-state physics textbooks such as Kittel (1986) and Ashcroft and Mermin (1985), which have too little information, and monographs as well as journal articles, which are too much to read. For more details, the book of Zangwill (1988) is helpful. 

Peptides containing an N-terminal aminooxy group, a Cys residue, or even a C-terminal hydrazide can be generated readily by standard solid-phase peptide synthesis on commercially available supports, and can be used as partners in one or other of the above-mentioned reactions. In contrast, introduction of the appropriate reactive end at the C-terminus of a large peptide or a protein is much more difficult, but is illustrated in a few examples below. 

Owing to its single composition and pure covalent bonding, diamond is a standard solid material, and takes the role of the most appropriate sample in explaining the effects upon structure-sensitive properties when the structure of solid material deviates from the ideal state. 

Doty Scientific, Inc. (Columbia, SC, USA) has been relatively successful in incorporating high resolution capabilities into their more standard solid-state MAS probes,32 where, in a traditional application, the extra care may not ever be noticed, but it provides the ability to use one MAS probe for both solid and gel-phase samples. They have introduced a sample insert that permits ready preparation of a number of samples that can be inserted into a MAS rotor for spectral acquisition, then preserved (or discarded) without requiring the dedication of a more expensive rotor. 

The Fc-modified uridine was incorporated into DNA trinucleotides with standard solid-phase synthesis. An interesting Fc conjugate has also been reported recently having an Fc group linked to two nucleobases such as thymine/uracil. These conjugates form supramolecular assemblies by base paring directed self-assembly.92... 

Because thioether formation is a rapid, irreversible reaction, it has been widely used for the macrocyclization of peptides or peptoids on supports (Entries 1-4, Table 8.5 [62]). For this purpose, either S-protected cysteine or S-protected co-aminomercap-tans are linked to a support and then elongated by standard solid-phase peptide/pep-toid chemistry. When a suitable length has been reached, the terminal amine is acy-... 

Standard solid-phase peptide synthesis requires the first (C-terminal) amino acid to be esterified with a polymeric alcohol. Partial racemization can occur during the esterification of N-protected amino acids with Wang resin or hydroxymethyl polystyrene [200,201]. /V-Fmoc amino acids are particularly problematic because the bases required to catalyze the acylation of alcohols can also lead to deprotection. A comparative study of various esterification methods for the attachment of Fmoc amino acids to Wang resin [202] showed that the highest loadings with minimal racemization can be achieved under Mitsunobu conditions or by activation with 2,6-dichloroben-zoyl chloride (Experimental Procedure 13.5). iV-Fmoc amino acid fluorides in the presence of DMAP also proved suitable for the racemization-free esterification of Wang resin (Entry 1, Table 13.13). The most extensive racemization was observed when DMF or THF was used as solvent, whereas little or no racemization occurred in toluene or DCM [203]. 

In the studies described below cyclic head-to-tail peptides were synthesized by standard solid-phase synthesis utilizing Boc chemistry 27 All syntheses were carried out with Boc-Pro-phenylacetamidomethyl resin. The use of Pro as the C-terminus residue was required so as to prevent racemization during the cyclization reaction (see Section 13.3.1.1). 

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